Articles > New Method To Analyze Marine Microbe DNA

New Method To Analyze Marine Microbe DNA

May 23, 2007 — Drs. Michael Sieracki and
Ramunas Stepanauskas, scientists at Bigelow Laboratory, have proven a
new approach of obtaining genetic codes of ocean microbes, based on the
analysis of individual unicellular organisms.

"The microbes in the oceans control most major chemical cycles in
the biosphere, yet we know very little about how they work or who they
are. Finding a reliable and economical way of accessing genomes of the
uncultured microorganisms is one of the biggest challenges facing
environmental microbiologists today", said Dr. Sieracki.

Over 99% of the Earth’s microorganisms cannot be cultivated in
laboratory, making their ecological roles, biochemistry and potential
practical applications an unresolved mystery. The cutting-edge approach
to tackle this enigma, originally developed for the human genome
sequencing project, has been sequencing large quantities of short
sections of DNA from the extracts of entire microbial communities, and
then assembling these sections back into individual genomes by
computational means.

Unfortunately, the diversity of natural microbial communities proved
so incredibly high, that very few genomes could be assembled from even
the largest metagenomic studies, consisting of millions of DNA
sequences. In a paper published this month in the Proceedings of the
National Academy of Sciences, Drs. Stepanauskas and Sieracki propose an
alternative to the metagenomic research.

"We present a novel approach to studying metabolic capabilities of
the uncultured microbial taxa. Our method is based on
fluorescence-activated sorting, whole genome amplification, and
multi-locus DNA sequencing of single cells. This allows us to sequence
any number of genes in each cell, including those that reveal cell’s
identity and those that tell us what biochemical reactions the cell is
capable of performing", said Dr. Stepanauskas.

The publication "Matching phylogeny and metabolism in the uncultured
marine bacteria, one cell at a time," is a result of the researchers’
collaboration, which has developed since Dr. Stepanauskas arrived at
Bigelow in 2005. "The availability of the first flow cytometry facility
dedicated to ocean science, which is headed by Dr. Sieracki, was one of
the reasons behind my move to Bigelow", said Dr. Stepanauskas. 

Source :Bigelow Laboratory for Ocean Sciences

 


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